I feel like people are taking the "he's a she" line completely out of context, so allow me to explain. During Wicked Eyes and Wicked Hearts, Sera makes some passing comments on the present nobles, which is presumably information that she got by talking to the servants. Iirc Sera says something about how one of the nobles mistreats his servants, how they are all a 'fun, close marrying crowd' and she also mentions that a certain 'he' is actually a 'she'.

But I really don't think that this refers to a trans man, I just assumed that one of the noble women was disguised as a man during the ball, either to conceal her identity or maybe just for fun. So no, I personally don't believe that Sera is actually transphobic based on this one line of dialogue. But you'll have to judge for yourself what you think that line means.